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exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants
https://exomiser.readthedocs.io
GNU Affero General Public License v3.0
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Run stand-alone hiPHIVE prioritization #360

Open edg1983 opened 4 years ago

edg1983 commented 4 years ago

Hi,

I'm wondering if it is possible to run the hiPHIVE prioritization as a stand-alone tool providing a list of HPO terms. Basically, I want to get a list of all genes with the associated hiPHIVE pheno score based on the input HPOs, without providing any variant.

PabloBotas commented 4 years ago

Hi! This is also a question I had. It would be useful to be able to re-evaluate a given VCF with pathogenicity already calculated over a new/evolved set of HPO terms. We had faced the situation of cases running exomiser, then realizing that they missed some HPO terms and having to re-run everything again. Could it be possible to bypass the variant pathogenicity evaluation?

julesjacobsen commented 4 years ago

Hi Pablo,

You could try running the analysis with all the usual filters, but set the inheritanceModes to be empty: inheritanceModes: {} save the output file in VCF format.

You will then need to re-analyse the output filtered VCF file twice more - once using the original HPO terms (should give you your original results) and again using a different set of HPO terms. This time re-enable the inheritanceModes with all the default options as provided in the example yaml file.

This won't disable the pathogenicity or read it from the first filtered VCF, but it will dramatically cut-down on the run-time for the second analysis.

I'd like to bring to your attention that this isn't the usual way to run things and has NOT been, tested so if you do want to do this please test things and if you find any issues (or indeed no issues) please report back.

PabloBotas commented 4 years ago

Thanks @julesjacobsen, I am still not sure about the logic you suggest. But I will definitely give it a try as soon as possible and come back with answers (and possibly some questions). Thanks!